Changes in src/boundary.cpp [b998c3:d6eb80]

File:

• src/boundary.cpp (modified) (8 diffs)

src/boundary.cpp

@@ -19 +19 @@
 
 #include<gsl/gsl_poly.h>
+#include<time.h>
 
 // ========================================== F U N C T I O N S =================================
@@ -654 +655 @@
  * \param *out output stream for debugging
  * \param *mol molecule with atoms and bonds
- * \param *&TesselStruct Tesselation with boundary triangles
+ * \param *TesselStruct Tesselation with boundary triangles
  * \param *filename prefix of filename
  * \param *extraSuffix intermediate suffix
  */
-void StoreTrianglesinFile(const molecule * const mol, const Tesselation *&TesselStruct, const char *filename, const char *extraSuffix)
+void StoreTrianglesinFile(const molecule * const mol, const Tesselation * const TesselStruct, const char *filename, const char *extraSuffix)
 {
         Info FunctionInfo(__func__);
@@ -789 +790 @@
  * \param configuration contains box dimensions
  * \param distance[NDIM] distance between filling molecules in each direction
+ * \param boundary length of boundary zone between molecule and filling mollecules
+ * \param epsilon distance to surface which is not filled
  * \param RandAtomDisplacement maximum distance for random displacement per atom
  * \param RandMolDisplacement maximum distance for random displacement per filler molecule
@@ -794 +797 @@
  * \return *mol pointer to new molecule with filled atoms
  */
-molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, double distance[NDIM], double RandomAtomDisplacement, double RandomMolDisplacement, bool DoRandomRotation)
+molecule * FillBoxWithMolecule(MoleculeListClass *List, molecule *filler, config &configuration, const double distance[NDIM], const double boundary, const double RandomAtomDisplacement, const double RandomMolDisplacement, const bool DoRandomRotation)
 {
         Info FunctionInfo(__func__);
@@ -817 +820 @@
   for (MoleculeList::iterator ListRunner = List->ListOfMolecules.begin(); ListRunner != List->ListOfMolecules.end(); ListRunner++) {
     Log() << Verbose(1) << "Pre-creating linked cell lists for molecule " << *ListRunner << "." << endl;
-    LCList[i] = new LinkedCell((*ListRunner), 5.); // get linked cell list
-    if (TesselStruct[i] == NULL) {
-      Log() << Verbose(1) << "Pre-creating tesselation for molecule " << *ListRunner << "." << endl;
-      FindNonConvexBorder((*ListRunner), TesselStruct[i], (const LinkedCell *&)LCList[i], 5., NULL);
-    }
+    LCList[i] = new LinkedCell((*ListRunner), 10.); // get linked cell list
+    Log() << Verbose(1) << "Pre-creating tesselation for molecule " << *ListRunner << "." << endl;
+    TesselStruct[i] = NULL;
+    FindNonConvexBorder((*ListRunner), TesselStruct[i], (const LinkedCell *&)LCList[i], 5., NULL);
     i++;
   }
@@ -835 +837 @@
   FillerDistance.Init(distance[0], distance[1], distance[2]);
   FillerDistance.InverseMatrixMultiplication(M);
-  Log() << Verbose(1) << "INFO: Grid steps are ";
-  for(int i=0;i<NDIM;i++) {
+  for(int i=0;i<NDIM;i++)
     N[i] = (int) ceil(1./FillerDistance.x[i]);
-    Log() << Verbose(1) << N[i];
-    if (i != NDIM-1)
-      Log() << Verbose(1)<< ", ";
-    else
-      Log() << Verbose(1) << "." << endl;
-  }
+  Log() << Verbose(1) << "INFO: Grid steps are " << N[0] << ", " << N[1] << ", " << N[2] << "." << endl;
+
+  // initialize seed of random number generator to current time
+  srand ( time(NULL) );
 
   // go over [0,1]^3 filler grid
@@ -859 +858 @@
           // get linked cell list
           if (TesselStruct[i] == NULL) {
-            eLog() << Verbose(1) << "TesselStruct of " << (*ListRunner) << " is NULL. Didn't we pre-create it?" << endl;
+            eLog() << Verbose(0) << "TesselStruct of " << (*ListRunner) << " is NULL. Didn't we pre-create it?" << endl;
             FillIt = false;
           } else {
-            FillIt = FillIt && (!TesselStruct[i]->IsInnerPoint(CurrentPosition, LCList[i]));
+            const double distance = (TesselStruct[i]->GetDistanceSquaredToSurface(CurrentPosition, LCList[i]));
+            FillIt = FillIt && (distance > boundary*boundary);
+            if (FillIt) {
+              Log() << Verbose(1) << "INFO: Position at " << CurrentPosition << " is outer point." << endl;
+            } else {
+              Log() << Verbose(1) << "INFO: Position at " << CurrentPosition << " is inner point or within boundary." << endl;
+              break;
+            }
             i++;
           }
@@ -931 +937 @@
       }
   Free(&M);
+
+  // output to file
+  TesselStruct[0]->LastTriangle = NULL;
+  StoreTrianglesinFile(Filling, TesselStruct[0], "Tesselated", ".dat");
+
   for (size_t i=0;i<List->ListOfMolecules.size();i++) {
         delete(LCList[i]);